WHO ARE THEY?
Nitrifying bacteria are Gram negative, obligate aerobic chemolithotrophs
which oxidize ammonium to nitrite or nitrite to nitrate as their sole
energy source and assimilate carbon dioxide via the Calvin Benson cycle.

Nitrifying
bacteria are not phylogenetically diverse; the capability is restricted
to a small group of organisms, most of which are closely related to each
other. Bacterial systematics analysis of 16S rRNA has demonstrated that
there are two phylogenetically distinct groups of autotrophic ammonium-oxidizing
bacteria, both within the class Proteobacteria. One group within the gamma
subclass and the other group represents a family within the beta-subclass.

WHAT
DO THEY DO?
The ecological importance of ammonium-oxidizers and nitrite oxidizers
lies in their role in the biological oxidation of reduced nitrogen compounds,
often leading to the removal of nitrogen from the environment via denitrification.
In many aquatic systems, especially shallow systems and sediment water
interfaces, denitrification depends directly on NO3 supplied from nitrification.
Thus, the environmental factors that control nitrification also control
denitrification, as documented for regions of Chesapeake Bay. Although
nitrifiers have been isolated from diverse environments and are generally
ubiquitous in soils, freshwater and marine environments, they account
for a very small proportion of the total bacterial population in natural
environments.

HOW
DO WE STUDY THEM?
In this porject we will be documenting their biodiversity and assessing
their ecological importance along several environmental gradients in the
Choptank River, Chesapeake Bay and the Sargasso Sea. Since they are not
numerically abundant, we will use sensitive and specific methods of detection
and identification based on nucleic acid analysis.

Phylogeny
and functionality are linked for the nitrifiers, much more so than for
denitrifiers or other organisms important in specific steps in nitrogen
cycling. For this reason it has been possible to use 16S rRNA. However,
we will employ functional genes for identification in this study with
the added advantage of assessing activity by measuring mRNA. The key enzyme
in ammonium oxidation is ammonia-monooxygenase (AMO) and its sequence
diversity, although greater than that derived from 16S rRNA, aligns closely
with it. Sequences from the public databases, augmented by those from
our large culture collection of nitrifying bacteria (Ward laboratory)
will be used to develop the suite of probes to be deployed on the gene
arrays.